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The Genomic Repairman is currently a Ph.D. student who escaped from the deep south, and studies DNA damage and repair through biochemical and genetic approaches. He intends to use pine away about his scientific interests and rant about the things (and there are lots of them) that annoy him.

My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

So here is a guest post from Thomas Joseph, a guy who I have been following for almost a year. He is insightful, got a solid message, and has left nothing but inspiring words of encouragement on my blog since I began trolling on his over a year ago. So give a big round of applause the guy!

Disclaimer: If you recognize yourself in this tale, it’s pure coincidence. Yes, the world of science is small, but not THAT small. And if I really am talking about you, don’t worry … I didn’t mention any names. Oh, and I may have embellished a tad in some spots, probably because James Frey was my ghost writer, and partly because it sounds a lot cooler that way. See what I did there? I embellished … James Frey wasn’t my ghost writer, just my muse.

If you’re like me, you cringe every time you hear someone say “Oh, this will be an easy pub!” Often it’s a graduate student caught up in the hype of their new project and enamored with the idea of the LPU (least publishable unit). These comments are also generally stated on the heels of said individual perusing some D-tier online-only, open access journal which has a total of two issues and will probably close before the end of the year … but whatevs … they’re still peer-reviewed!

Sometimes I catch myself making this claim, and while it still makes me wince when I say it, there are instances where I think it has the possibility of being true. This tale relates one such account.

It all started back when we were working on our forecasted project plan. This forecast covers several years, and within that plan we are supposed to document what publications we plan on producing out of the project over that period of time. So I wrote up my sections (all of which were approved on the first go around … thankyouverymuch) and listed my publications. I included several of my collaborators, as they were obviously going to contribute. Our leader synthesized everyone’s contributions, merged it into a single document and passed it along to us. I reviewed it, and when I came to the publications list noticed that I was the only researcher who WASN’T collaborating on any other publications.

Whiskey. Tango. Foxtrot. Here I was, including my collaborators in my projects and all I managed to get was a good f**k up the ass from them … without a single wrap around. That’s thanks for you, eh? So I went to the leader of the project and broached the subject with him.

Me: Hey, how come I have no second authors out of this project?Him: You have plenty of first authors.Me: Yeah, I know, because I’ll be writing them all, and I’ve included a bunch of you dudes on them as well. Where’s my love from you guys?Him: I wouldn’t worry about that right now, it’ll sort itself out.Me:Ok, we’ll see about that.

So the end of the year comes and my boss comes to me and asks me how things are looking for NEXT year. I tell him I have my first authors all lined up, and then he asks me about second authors. Second authors are nice because while your first authors will get you a satisfactory rating, getting a bunch of second authors could get you a quicker promotion (it’s all about bulk), or at the very least a nice bonus at years end. It also makes our boss look good because his scientists are all kick-ass, super productive robots who shit publications. I tell him I have … NONE. NONE? Yep, NONE. Why? I was told not to worry about it. Well, you better worry about it. Yah, figures. Thanks.

So I go off to scramble up a second author somewhere. Fortunately there is an individual at work who has taken me under their wing. Ok, it’s more along the line of me squeezing my way underneath it, but I’m there underneath that wing at any rate, and it’s really the end result that’s most important right? So I go to them and ask them if they have any microbial work they need done on a project. Turns out they do. They’d like to know the ratios of two microbes in the environment they’re looking at, and they ask me if I could do something about that. I tell them I’ll get back to them.

Now, I’m a molecular biologist by trade, and I thought that perhaps there might be a way to do it using a conventional technique we routinely do. However, the gold standard really is, from what I can tell, something we’ve never done before. It’s a very sensitive procedure, and will be able to tell us all sorts of things, but it’s not going to be via a PCR-based assay. There is another hitch. We don’t have the equipment. Plus my lab is already at the straining point. We have samples dropped on us weekly, and it’s not just one or two samples. Usually it’s a dozen or so, sometimes a couple dozen if we’re [sarcasm]lucky[/sarcasm]. The project my colleague was speaking of was at least three to four dozen samples, all of which would need to be processed in a way we’ve never done before. But … what if I could contract the work out? Then, all I’d need to do was collect the samples, ship them out, pay a fee, and get my data. Sweet.

Easy pub.

It seemed like such a nice deal. I’d pay someone else do to the sample prep, run the analysis, and ship me the data. I’d crunch it, synthesize it, run all the fancy statistics, and come up with something that made sense. Make a table or two, send it to my collaborator and see the work incorporated into a publication. I save a lot of time by contracting, and I get a second author out of it.

But I jinxed it, said it was going to be an easy pub, and the science gods cursed me. It started out easy enough I tell you, but I quickly realized that things were going to get ugly. Of course, since you’re reading this you know it must sort of end well … like when a character is narrating a movie and it looks like they’re about to die, but you know they can’t because they wouldn’t be narrating?

So I collected my samples, kissed them goodbye, tucked them into a box, and shipped them off. And waited. And waited. And waited. And … well, waited a really long time. So long that my collaborators had forgotten I collected samples and wanted to let me know that I should really go out and get this work started. I began to panic. What was my backup plan. Well, I didn’t have one. I had a fuckton of sample left, because I’m paranoid about not having enough sample to finish a project … but I really didn’t want to send this stuff off to another lab. There were two reasons why I didn’t want to do this. First, the next cheapest lab wanted to charge more than the lab we contracted with. By a substantial amount. Like quadruple. Second, I had sort of paid the first lab thinking I was going to get my data quickly. This is really a no-no, but I went and did it anyway. I mean, what was the chance that they wouldn’t come through?

After several months the possibility that they wouldn’t come through seemed pretty high. I started building a brick house from all the ones I was shitting. Emails went unanswered, and my collaborators informed me of a meeting I’d have to attend to present data I still hadn’t received. Oy vey. This was going to be a bit difficult to explain.

Then one day, my data arrived. No fanfare, just sitting there in my inbox. It had arrived in a very unassuming envelope, with just my name and address on it. No return address. I clutched at it as if my life and career had depended upon it (it sort of had), raced to my office and popped it into the CD drive. There was the data, all of it. Glorious, glorious data! And an executable file. Guess it was up to me to get this installed and get the data analyzed. Did the installation and opened up the first file.

Now, this program was originally designed for Windows 3.0 or some shit. You moused over an icon and it didn’t tell you jack. Better yet, I’d click on the Help pull down and it’d tell me the damn index and help menu didn’t install. Great. Went to the dealer to look for an online manual I could download in PDF format. Nada. Guess I was flying blind. No biggie, I’d just start clicking on icons like a monkey (with Tourette’s obviously, considering my behavior every time my mashing caused the program to crash) and see what I got. Eventually I’d figure it out, I mean I’m edumacated and all … may as well put all that accrued student loan money to good use.

So after endless hours of cursing, crying, pleading, and killing endless trees by mistakenly printing reams of useless reports I got the hang of it all. Now came the fun part. Identifying the elements that were integral for my project. It seemed pretty easy, I mean they had run several standards alongside my samples, so I could just compare and contrast. But there was one slight problem. The standards don’t have every single element I needed to look for. Reading the literature, it’s obvious that some elements are couched between other elements (which were in the standards), so those would be easy to pick out. But that wasn’t always the case.

Figure: Life sometimes really hates me.

I did finally manage to figure everything out, get my spreadsheets all nice and pretty and get all several dozen samples analyzed. Still working on the statistics (using SAS is another tale in and of itself) but we’re now on the homestretch. However, this project, while it may have been relatively less work than something that would typically occur in my lab, was not the piece of cake I thought it would be. Will I still get a pub out of it? Yes I will. Did I enjoy the experience: Most definitely not. So I offer it as a cautionary tale, and as a reminder to myself next time I come up with a plan for an “easy pub”.

That damn software was buggy as all get out. I finally managed to get the hang of it, for the last six samples ... but meh ... at least it's done now!

I didn't even mention that when I wanted to save an excel sheet of my peaks, I had to PRINT. There was no save option, there was no export option (into an .xls format). Instead, I had to "Print to File" and when I clicked "Ok" ... NOTHING HAPPENED. Oh, it saved a file ... just didn't tell me where. Took me about 10 minutes to track the damn files down the first time. Mother McRee, I hate that software.

Ha! I just received the worst possible review ever from a paper we sent to the worst possible journal ever. Not that the manuscript was bad, it was just sort of...meh... but the results (produced by an undergrad) were solid. Whoever reviewed our paper had 80 comments, yes 80. Ranging from the moderately useful: this statistical test would be more appropriate (maybe), to completely inane: some of the references are too old and cannot be found online (WTF!) or I don't like the font on this axis in FIgure 3D (Fuck you!). I agree, the easy pub is a myth.

Namnezia you bring up a great point about old references. Who cares if its not online, those are the folks that did the work and thus deserve the credit. If they want to fact check you they can get off their sorry lazy asses and do an interlibrary loan to get ahold of those articles. 80 comments, you must have had a newbie reviewer!

My grad PI was notorious for the "easy pub" or the "If you get this to work, it'll be in Science!" I learned to just ignore him after spending a year of my life trying to get data for 2 "easy pubs" that never panned out :P

The tale of this story gets even better. I've finally gotten the data all sorted, and stats run (SAS ... gah!) So my collaborator and I sat down to discuss it, and figure out what it all meant. So I tell him "You're writing this up this year?" and he looks at me like I have five heads and says "You're lead on this!"

Excuse me? Where is my 2nd author pub? The one with minimal input and maximum credit? Jimminy Christmas! And second ... he's decided we really need a second year in the study. I suppose that's really not a problem because the lab that did this work for us took about 6 months to get our results back so we're looking at only a couple of months before the next sampling point to space them roughly 11-12 months apart. But crikey ... this thing becomes "less easy" by the minute.

Re-reading this article and I have to think ... I'm obviously an idiot.